Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Miya:8500849 Length = 366 Score = 150 bits (379), Expect = 5e-41 Identities = 112/313 (35%), Positives = 159/313 (50%), Gaps = 18/313 (5%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 + L I K GA L +SL + G LLG + GKT L+R++AG + P AG +++ Sbjct: 4 ITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTISIG 63 Query: 63 GKDVTG------MPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDA--RVREI 114 G+ V+ +P R++ +V+Q + +P M VA NI PLKL G + +V E Sbjct: 64 GEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQVLET 123 Query: 115 ASRLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELT 174 +++ +R P++LSGGQQQRVALARAL LMLLDEPL NLD LREE+R E+ Sbjct: 124 VEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRFEIK 183 Query: 175 QLFAAGQSTVVYATTEPGEALLLGGYTAVLDE-GQLLQYGPTAEVFHAPNSLRVARAFSD 233 +L T++Y T + AL + A++D G + Q G E+F P V R Sbjct: 184 ELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFRFMG- 242 Query: 234 PPMNLMAASATAQGVRLQGGAELTLPLPQGA--ATAAGLTVGVRASALRVHARPGDVSVA 291 N + A + GG + P+P G A G R S +R+ AR GD + Sbjct: 243 -VANFLPARRRGMAMLAAGGEQ---PVPWGLPDGDAEHWMAGFRPSDVRL-ARQGD-GLR 296 Query: 292 GVVELAEISGSDT 304 G V A G+ T Sbjct: 297 GTVRRASFLGAMT 309 Lambda K H 0.318 0.133 0.375 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 282 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 363 Length of database: 366 Length adjustment: 29 Effective length of query: 334 Effective length of database: 337 Effective search space: 112558 Effective search space used: 112558 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory